tbuckley/cabot-search huggingface dataset:
BIOM-56. THE PRIVATE AND RECURRING ANTIGENIC PROFILE OF MOST AGGRESIVE PEDIATRIC BRAIN TUMORS
Authors: Changlin Yang, Vrunda Trivedi, Oleg Yegorov, Duane Mitchell
Journal: Neuro-Oncology (2023)

Abstract BACKGROUND Efficient immunotherapies for pediatric brain tumors face a significant challenge in identifying tumor rejection antigens. To overcome this hurdle, we utilized a comprehensive computer algorithm called the Open Reading Frame Antigen Network (O.R.A.N.). METHODS Our focus was on expressed epitopes, including single nucleotide variations, small indels, gene fusions, novel junctions from alternative splicing, and Tumor Associated Antigens (TAAs), for antigenic epitope predictions. To ensure uniqueness, we compared immunogenic TAA epitopes against a personalized human proteomic library, ensuring they were not shared by other expressed isoforms or genes. The immunological landscape of medulloblastoma (n = 170) and DIPG (n = 30) was explored using immune deconvolution techniques combined with single-cell RNA sequencing integration. RESULTS Our hypothesis was that medulloblastomas and DIPG exhibit diverse immune profiles and express genes that are rarely found in normal tissues, making them potential targets for immunotherapy. In this study, we found that most neoantigens identified in medulloblastoma patients were unique to each individual, emphasizing the need for personalized neoantigen-based therapies. Interestingly, recurring neoantigens were predominantly present in the MB SHH subgroup, while they constituted only a small fraction of putative antigens in WNT, Group 3, and Group 4 patients. On the other hand, recurring Tumor Associated Antigens (TAAs) were more frequently expressed in the latter three molecular subgroups but not in the SHH subgroup. Thus, a combination of personalized neoantigen vaccines and targeting recurring TAAs could potentially maximize the anti-tumor effects. CONCLUSION Medulloblastoma is a disease characterized by its heterogeneity, and current standard treatments do not adequately address this aspect. In the case of DIPG, surgical resection is not a viable option due to its diffuse and infiltrative nature within the brainstem. By leveraging the power of the immune system, cellular immunotherapy holds promise in providing more targeted and personalized treatment options for pediatric brain tumor patients.
CTIM-02. PHASE 2 TRIAL OF PEMBROLIZUMAB FOR PATIENTS WITH BRAIN METASTASES OF DIVERSE HISTOLOGIES
Authors: Priscilla Brastianos, Albert Kim, Anita Giobbe-Hurder, Eudocia Lee, Nancy Lin, Beth Overmoyer, Patrick Wen, Lakshmi Nayak, Justine Cohen, Jorg Dietrich, April Eichler, Rebecca Heist, Ian Krop, Donald Lawrence, Jennifer Ligibel, Sara Tolaney, Erica Mayer, Eric Winer, Brittany Bent, Magali de Sauvage, Nazanin Ijad, Juliana Larson, Braxton Marion, Sally Nason, Naina Murthy, Elizabeth Summers, Sherry Ratcliffe, Maura Mahar, Helen Shih, Kevin Oh, Daniel Cahill, Elizabeth Gerstner, Ryan Sullivan
Journal: Neuro-Oncology (2023)

Abstract BACKGROUND Patients with brain metastases have limited treatment options.The PD-L1/PD-1 pathway is an immune suppressive mechanism in brain metastases. METHODS This was a single-arm phase 2 clinical trial evaluating the intracranial efficacy of pembrolizumab, a PD-1 inhibitor, in patients with brain metastases. The target accrual was 58 patients to achieve at least 52 evaluable patients. The primary endpoint was intracranial benefit (complete response, partial response, or stable disease by modified RANO criteria). The study design compared a null intracranial benefit rate of 10% against an alternative of 24%. If at least 8 patients among 52 had intracranial benefit, the primary efficacy endpoint would be met and pembrolizumab would be considered worthy of further study (type-I error of 10%, power of 89%). RESULTS In 57 evaluable patients, median age was 53 (range 28-80). Tumor histologies included breast (n = 35), NSCLC (n = 7), melanoma (n = 2), small-cell lung cancer (n = 2), sarcoma (n = 2), and other (n = 9). For patients with breast cancer, 16 patients had HER-2 positive, 17 had hormone-receptor positive and 11 patients had triple-negative disease. The study met its primary endpoint and achieved an intracranial benefit rate of 42.1% (90% confidence interval [CI]: 31-54%). Thirty-seven percent of breast cancer patients (90% CI: 24–52%) and 43% of NSCLC patients (90% CI: 13–77%) had intracranial benefit. All four breast cancer subtypes derived efficacy from pembrolizumab. Seven patients, who had either breast cancer, melanoma or sarcoma, had overall survival &amp;gt;2 years. The extracranial benefit rate in patients with evaluable extracranial disease based on RECIST 1.1 criteria was 45% (90% CI: 31-59%). Median overall survival was 8.0 months (90% CI: 5.5-8.7 months). Grade 4 toxicities at least possibly related to treatment were observed in 2 patients: cerebral edema. CONCLUSIONS Our study of pembrolizumab met overall primary endpoint for intracranial benefit in patients with brain metastases across diverse histologies.
IMMU-52. LOW-INTENSITY PULSED ULTRASOUND CONDUCTS ANTIGEN-INDEPENDENT T CELL HOMING INTO THE BRAIN PARENCHYMA WITH THE INTACT BLOOD-BRAIN BARRIER
Authors: Marco Gallus, Atsuro Saijo, Jeffrey Haegelin, Pavlina Chuntova, Akane Yamamichi, Senthilnath Lakshmanachetty, Hideho Okada
Journal: Neuro-Oncology (2023)

Abstract The blood-brain barrier (BBB) protects the brain parenchyma from excessive inflammation but also leads to poor immune cell homing, hampering the success of immunotherapies, such as ones for low-grade glioma, where the BBB is intact. Low-intensity pulsed ultrasound (LIPU) combined with the application of microbubbles allows the non-invasive, transient opening of the BBB and recent studies have observed immune cell infiltration into malignant gliomas following LIPU. While these data warrant mechanistic investigations on the effects of LIPU in preclinical settings, most mouse models of malignant glioma already display BBB disruption. Therefore, to study whether LIPU affects antigen-specific immune cell trafficking through the BBB, we created a novel immunocompetent mouse model of non-tumor bearing mice that display an intact BBB and express a minigene cassette encoding for four immunogenic peptides in glia cells under the glial fibrillary acidic protein (GFAP) promotor. These peptides are either presented by major histocompatibility complex (MHC) class I: human melanoma antigen glycoprotein (gp) 100 and lymphocytic choriomeningitis virus (LCMV)gp31) or class II: LCMV gp66 and tyrosinase-related protein 1. Minigene expression in astrocytes induced antigen-specific T cell proliferation and Interferon-γ release in vitro. Intravenous adoptive T cell transfer of naïve or respectively CD3/CD28-coactivated antigen-specific CD 8 T cells targeting gp100 peptide followed by immediate LIPU treatment induced T cell homing into the CNS parenchyma, and astrocyte-T cell interaction was confirmed by ex-vivo two-photon imaging. Furthermore, some animals that underwent immediate LIPU treatment after transfer of preactivated antigen-specific T cells developed neurological deficits such as ataxia, while no deficits were observed in those animals that underwent LIPU but did not receive T cells or received activated T cells but did not undergo LIFU treatment. In conclusion, LIPU might be a novel effective tool to support antigen-independent immune cell homing with the intact BBB.
DDEL-03. PHYSIOLOGICALLY BASED PHARMACOKINETIC (PBPK) MODELING OF HETEROGENEOUS DRUG PENETRATION INTO THE HUMAN BRAIN AND GLIOBLASTOMA
Authors: Jing Li, Nader Sanai, Artak Tovmasyan, Seongho Kim
Journal: Neuro-Oncology (2023)

Abstract BACKGROUD Insufficient penetration of potentially effective therapeutic agents across the human blood-brain barrier (BBB) is a hurdle to the effective treatment of brain cancer. The BBB in glioblastoma is disrupted to varying extents. This study was to develop a PBPK model platform for prediction of heterogenous drug penetration into the human brain and glioblastoma. METHODS A 7-compartment CNS (7-CNS) PBPK model platform was developed to predict drug concentrations in the brain blood, brain parenchyma, cranial CSF, spinal CSF, and 3 tumor compartments representing infiltrating tumor (T1) with a slightly disrupted BBB, bulk tumor (T2) with a leaky BBB, and necrotic core (T3) with no blood vessels. The model accounted for brain/tumor general anatomy and regional pathophysiological differences. Drug transfer and fluid balance between compartments were described by differential equations. Simulations were performed using R programming. The model was verified by comparisons of predicted and observed tumor PK data of ribociclib and abemaciclib in glioblastoma patients. RESULTS For ribociclib, the model-predicted mean unbound drug brain-to-plasma ratio (Kp,uu) was 0.17, 2.2, 8.2, 24.9 in normal brain, T1, T2, and T3, respectively; the predicted Kp,uu in T1 and T2 was consistent with observed Kp,uu in non-enhancing (median, 2.0) and enhancing tumors (median, 10.1) from 12 patients. For abemaciclib, the predicted mean Kp,uu was 0.88, 1.4, 6.2, and 3.1 in normal brain, T1, T2, and T3, respectively; the predicted Kp,uu in T1 and T2 agreed with observed Kp,uu in non-enhancing (median, 2.1) and enhancing tumors (median, 7.2) from 38 patients. CONCLUSION The developed PBPK model platform well predicts heterogeneous drug penetration and distribution in normal human brain and different regions of glioblastoma, as verified by ribociclib and abemaciclib. It provides a mechanism-based computational modeling tool to assist the development and design of improved drugs and dosing regimens for more effective treatment of glioblastoma.
DNAR-07. MOLECULAR BIOMARKERS ASSOCIATED WITH TARGETED DISRUPTION OF ALTERNATIVE LENGTHENING OF TELOMERES IN ATRX-DEFICIENT GLIOMA MODELS
Authors: Matthew Waitkus, Michael Brown, Christopher Pirozzi, Nathan Reynolds, Alexandrea Brown, Laura Strickland, Zachary Reitman, Steve Keir, Mustafa Khasraw, David Ashley
Journal: Neuro-Oncology (2023)

Abstract Alternative lengthening of telomeres (ALT) is a telomerase-independent mechanism of telomere maintenance that occurs in approximately 10-15 percent of all cancers. ALT enables the replicative immortality of cancer cells and is characterized by elevated levels of DNA replication stress and telomere-localized DNA double-strand breaks (DSBs). In gliomas, ALT frequently co-occurs with inactivating mutations in ATRX, which is thought to promote ALT induction by disrupting ATRX-mediated histone H3.3 deposition at telomeres, thus leading to telomere synthesis by homology-directed repair mechanisms. To identify potential therapeutic vulnerabilities specific to ALT-positive tumors, we identified candidate ALT-positive cancer cell lines in the Cancer Dependency Map (DepMap) dataset and validated the presence or absence of ALT phenotypic markers, including ALT-associated PML bodies (APBs) and nuclear foci of single-stranded telomeric DNA (ssTeloC). Comparing ALT-positive cells to all other cancer cell lines in the DepMap dataset, we identified the replication fork remodeling enzymes SMARCAL1 and FANCM as gene dependencies with the highest degree of ALT-specificity. To validate SMARCAL1 as an ALT-specific dependency, we used inducible RNAi to deplete SMARCAL1 in ALT-positive glioma cells. SMARCAL1 depletion caused a marked increase in the abundance and intensity of ssTeloC nuclear foci, as well as increased γH2AX abundance in ALT+ glioma cells but not telomerase-positive cells. Inducible SMARCAL1 depletion did not coincide with detectable increases in apoptotic markers (e.g. caspase-3 cleavage). However, SMARCAL1 depletion caused a significant increase in the abundance of nuclear abnormalities indicative of mitotic catastrophe (e.g. micronuclei, nucleoplasmic bridges, and fragmented/multilobular nuclei). In an orthotopic model of ALT-positive glioma, doxycycline-inducible RNAi targeting SMARCAL1 extended the median survival of tumor-bearing animals to 155 days compared to 111 days in the non-targeting control condition. These data validate the therapeutic targetability of SMARCAL1 in ALT-positive gliomas and support the development of small molecule SMARCAL1 inhibitors for treatment of ALT-positive tumors.
IMMU-56. TARGETING NONO IN GLIOMA VIROIMMUNOTHERAPY
Authors: Andrew Gillard, Dong Ho Shin, Hong Jiang, Xuejun Fan, Sanjay Singh, Virginia Laspidea, Jiasen He, Andres Lopez-Rivas, Akhila Parthasarathy, Martha Alonso, Frederick Lang, Juan Fueyo-Margareto, Candelaria Gomez-Manzano
Journal: Neuro-Oncology (2023)

Abstract Despite aggressive therapies, the median survival for glioblastoma (GBM) patients remains just 7-months after tumor progression. Oncolytic virotherapy is a promising approach to reprogramming the immunosuppressed microenvironment of GBMs facilitating anti-tumor immunity. Delta-24-RGD is an oncolytic adenovirus that has shown favorable results in phase I/II clinical trials (NCT00805376, NCT03178032 and NCT02798406). However, the immune response of the patient functionally cleared the virus, limiting its anti-cancer efficacy to a subset (~20%) of patients. It is known that Non-POU Domain Containing Octamer Binding (NONO) is overexpressed in gliomas and is associated with poor survival of patients. Using bulk RNA sequencing, we showed that the NONO pathway is upregulated 7 folds during adenoviral infection. These results were confirmed by western blot analyses that showed a significant increase in the expression of NONO after Delta-24-RGD infection. We detected cellular and viral members of the NONO interactome using mass spectrometry analyses. Immunoprecipitation assays confirmed those results and showed that NONO binds to adenoviral proteins during infection and associates with the foreign DNA sensor cyclic GMP AMP synthase (cGAS). Using shRNA knockdown, we showed that NONO was required to induce innate immune activation in response to adenovirus infection. Thus, we observed a 180-fold increase in type I interferon after the infection with the virus that was reversed in NONO-null cells. Therefore, NONO is a previously undetected innate immune sensor of adenoviruses in the nucleus. In addition, the fact that NONO binds adenoviral proteins suggests a new double-sensor mechanism involving the detection of both foreign DNA and viral proteins. Interactions between NONO and adenoviral proteins should be considered when designing the next generation of oncolytic adenovirus for the treatment of gliomas.
NIMG-41. ASSOCIATION BETWEEN PERFUSION IMAGING METRICS AND RADIO-PATHOMIC MAPS OF TUMOR PROBABILITY WITHIN AND BEYOND THE CONTRAST-ENHANCING VOLUME IN GLIOMA PATIENTS
Authors: Samuel Bobholz, Allison Lowman, Savannah Duenweg, Aleksandra Winiarz, Margaret Stebbins, Michael Flatley, Biprojit Nath, Fitzgerald Kyereme, Jennifer Connelly, Dylan Coss, Max Krucoff, Anjishnu Banerjee, Peter LaViolette
Journal: Neuro-Oncology (2023)

Abstract Perfusion MRI, using both contrast-based techniques such as dynamic susceptibility imaging (DSC) and non-contrast-based techniques like arterial spin labeling (ASL) have been used to monitor blood flow as a marker of angiogenic glioma presence, and showed substantial potential in the differentiation of true progression from pseudoprogression post-treatment. This study uses radio-pathomic maps of cellularity sensitive to areas of non-enhancing tumor to test the hypothesis that perfusion-derived markers of tumor probability will associate with tumor presence within contrast-enhancement but not beyond the enhancing margin. This study included pre-surgical relative cerebral blood volume (rCBV) estimates derived from DSC perfusion data from the PENN-GBM dataset (n=456) and presurgical ASL images from the UCSF-PDGM dataset (n=426) for analyses. The T1, T1C, FLAIR, and ADC images from each patient were used to generate radio-pathomic cell density maps using a previously validated model that excels at accurate detection of non-enhancing tumor presence. Mean cell density, rCBV, and ASL were computed for each corresponding patient within included segmentations for contrast-enhancement (excluding necrotic core) and FLAIR hyperintensity (excluding both necrotic core and enhancement). Pearson’s correlations were then used to quantify the association between perfusion-derived estimates and mean cell density within each region of interest. Both rCBV and ASL showed positive associations with cell density within contrast enhancement (rCBV: R=0.280, p&amp;lt; 0.001; ASL: R=0.117, p=0.016). However, both perfusion metrics also showed no association with cell density within the non-enhancing, FLAIR hyperintense region (rCBV: R=0.0162, p=0.731; ASL: R=-0.213, p=0.634). These results suggest that perfusion imaging successfully identifies angiogenic tumor but may be less efficacious in detecting non-enhancing tumor presence. Future studies should examine how perfusion’s relationship with hypercellular tumor presence evolves in the presence of treatment, as well as in relation to other advanced imaging metrics such as MR spectroscopy and CEST imaging.
DDDR-30. IDENTIFICATION OF DRIVERS OF RESISTANCE IN BRAFV600E PEDIATRIC HIGH-GRADE GLIOMA AND NOVEL THERAPEUTIC TARGETS
Authors: Rebecca Lehmann, Joshua Zhu, Chelsea Mayoh, Maria Tsoli, Benjamin Rayner, David Ziegler
Journal: Neuro-Oncology (2023)

Abstract The BRAFV600E mutation has recently been discovered as a driver mutation in a subset of pediatric high-grade gliomas (pHGG), with tumors driven by this mutation responding to targeted BRAF and MEK inhibitors. Unfortunately, resistance inevitability develops, resulting in disease progression. There is currently limited understanding of the mechanisms underlying drug resistance in BRAFV600E pHGG, and no effective counter-therapies exist. This study aimed to identify driver pathways of resistance in BRAFV600E pHGG and subsequently novel therapeutic targets. BRAF inhibitor-resistant, MEK inhibitor-resistant and BRAF+MEK inhibitor-resistant BRAFV600E pHGG cultures were derived through chronic exposure of a BRAFV600E patient-derived culture to vemurafenib (BRAF inhibitor), trametinib (MEK inhibitor) or a combination of both drugs, respectively. Cytotoxicity assays confirmed resistance. All resistant cell lines spontaneously changed from a spheroid phenotype to adherent growth, indicating changes in tumor characteristics. RNAseq identified &amp;gt; 1500 genes of interest, with subsequent Gene Set Enrichment Analysis identifying key pathways as novel drivers of resistance, the top-ranked gene sets being neural development and plasma membrane/cell adhesion. Approximately 45% of gene sets were enriched across all drug-resistant lines, indicating overlapping resistance mechanisms. Interrogation of the receptor tyrosine kinase (RTK) gene sets identified potent upregulation of several RTKs. Notably, overexpression of the RTK, EGFR, was confirmed through RNAseq and western blot as a potential key mediator of the acquired resistance. Combined treatment with vemurafenib and the EGFR inhibitor, dacomitinib, resulted in synergistic activity against both vemurafenib-resistant BRAFV600E pHGG cells and matched parental cells, providing a viable therapeutic option for drug-resistant BRAFV600E pHGG. Overall, novel drivers of resistance have been identified in BRAFV600E pHGG. EGFR overexpression was pinpointed as a key mediator and dual BRAF/EGFR inhibition displayed promising efficacy as a therapeutic option. Future studies will continue to elucidate the mechanisms of resistance using multi-omic approaches and the in vivo efficacy of dual BRAF/EGFR inhibition.
EPCO-50. THE TRANSCRIPTIONAL LANDSCAPE OF KEY INNATE DNA SENSORS WITHIN PRIMARY BRAIN TUMORS
Authors: Avani Mangoli, Michelle Bowie, David Ashley, Justin Low, Kevin Stevenson, Vidya Chandramohan, Seetha Hariharan
Journal: Neuro-Oncology (2023)

Abstract Primary brain tumors are notoriously resistant to immunotherapy. The efficacy of these treatments potentially requires normal expression of DNA innate sensors within both the immune and tumor compartments. Recently, we found that STING1, involved in the CGAS/STING pathway, is epigenetically silenced in the neoplastic cells of primary brain tumors. This silencing can be traced back to the normal brain. We and others have shown that rescue of STING1 expression can be modulated with epigenetic treatments. The mechanism by which DNA damage in cancer leads to an inflammatory response sheds light on the significance of other DNA sensors. We hypothesize that innate immune silencing within the tumor contributes to immunotherapy resistance and the addition of epigenetic treatments could increase efficacy. We evaluated the transcriptional landscape of DNA innate sensors within normal adult brain and in patient derived tumors including glioblastoma, pilocytic astrocytoma, and diffuse midline gliomas, H3K27M mutant. We found low expression of additional cytosolic DNA sensors including cGAS, AIM2, ZBP1 in normal neuronal as well as tumor cells. Since epigenetic silencing is modulated during normal development, we compared the transcriptional innate profiles from normal cortex brain development to primary brain cancers. DNA innate immune sensor expression correlates with pre-oligodendrocyte progenitor cells and oligodendrocyte progenitor cells. These results suggest the innate immune suppression of these key cytosolic DNA sensors is established early in fetal brain development and retained in the context of primary brain tumors. We are currently exploring the epigenetic profiles of fetal brain and brain tumors to determine how these innate immune expression patterns affect tumorigenesis and response to immunotherapy treatment.
NIMG-12. SPATIALLY MAPPING TREATMENT-EFFECT IN RECURRENT GLIOMA WITH PHYSIOLOGIC MRI AND DEEP LEARNING
Authors: Jacob Ellison, Nate Tran, Rany Hanna, Joanna Phillips, Anny Shai, Devika Nair, Annette Molinaro, Valentina Pedoia, Yan Li, Tracy Luks, Javier Villanueva-Meyer, Mitchel Berger, Shawn Hervey-Jumper, Manish Aghi, Susan Chang, Janine Lupo
Journal: Neuro-Oncology (2023)

Abstract INTRODUCTION Discriminating between glioma tumor recurrence (rTumor) and treatment-induced effects (TxE) from chemo and radiotherapy using MRI is an ongoing challenge in neuro-oncology. Although deep learning has been used to characterize suspicious lesions, these models typically do not account for lesions that are comprised of mixtures of rTumor and TxE components. We hypothesize that using an approach that includes using tissue samples with known location on MRI, incorporating perfusion-weighted and diffusion-weighted with anatomical MRI, self-supervised pretraining, and a novel ensembling strategy will improve performance and attain spatial maps of rTumor and TxE for determining subsequent treatment. METHODS Using 218 pathology confirmed tissue samples with coordinates on multi-parametric MRI from 111 patients with suspected tumor progression, we developed a deep learning approach to spatially map intratumoral regions of rTumor and TxE. Our model leveraged 10mm isotropic cubes centered on the tissue sample coordinates that includes Diffusion-Weighted and Dynamic Susceptibility-Contrast Perfusion MRI and large amounts of pathologically unlabeled data from the lesion in self-supervised pretraining. The multiple networks of the ensemble were generated through repeated constrained cross validation (RC-CV) which enabled unique repetitions of training with more variation in class proportions. RESULTS Our best classifier performed with a RC-CV/test AUROC of 0.85/0.81 and was able to generate maps of tumor probability as well as ensenble variance and uncertainty. Ensemble variance was significantly higher in prediction failures of rTumor (P=.006) and epistemic uncertainty was significantly higher (P=.002) in prediction failures of TxE in training. Test Performance dropped by 14.7% when removing self-supervised pretraining, 21.3% when removing physiological imaging contrasts, and 1.2% when ensembling across standard 4-fold CV. CONCLUSION The AUROC of .81 supports the feasibility of discriminating between TxE and rTumor within a single lesion non-invasively. Physiologic MRI, pretraining on pathology unlabeled data, and ensembling networks, improve performance and help characterize model failures.